Lowe is on Stuart Lancaster's list of potential England stars of the 2015 Rugby World Cup and the 22-year-old Harlequins centre proved why on the biggest stage club rugby has ever seen, with a crowd at Wembley of 83,761.
After Jordan Turner-Hall's try had put Harlequins ahead, Lowe produced a top class finish to score his side's second of the afternoon and Danny Care added their third after the break.
Saracens then threw the kitchen sink at Harlequins but Lowe kept the Premiership champions out with brilliant try-saving tackles on Michael Tagicakibau and Chris Wyles in the space of three minutes.
Harlequins were under siege and had three men sin-binned - Joe Marler, Care and Nick Easter - as they weathered wave after wave of Saracens attacks.
Richard Wigglesworth finally stole over when Marler and Care were both off the field and Owen Farrell added the conversion to his four first-half penalties.
That was enough to secure Saracens the losing bonus point and move them back up to second place - but Harlequins held out for the victory to open a six-point lead at the top.
This attendance beat the previous world record club attendance of 82,208, which was set in the 2009 Heineken Cup quarter-final between Leinster and Munster at Croke Park.
A total of 165,781 fans have watched the two Premiership matches between these London rivals this season, with Harlequins' 'home' game attracting 82,000 to Twickenham.
McFly provided the pre-match entertainment but it was Harlequins who caught the eye immediately after kick-off, with Turner-Hall scoring the opening try after just four minutes.
Nick Evans' clever flick to Tom Williams on the left touchline stretched the Saracens defence and Turner-Hall claimed the inside ball to crash over the line.
Williams' offload looked suspiciously forward but referee Gregg Garner confirmed the try and Evans, who has been in disappointing form with the boot in recent weeks, landed the conversion.
Harlequins were playing more rugby but they were also being penalised heavily by referee Garner, allowing Farrell to land three kicks to nudge Saracens ahead.
Things could have been worse for Harlequins had it not been for another sensational try-saving tackle, this time from the lock George Robson on Saracens wing James Short.
Saracens' lead was only temporary. Lowe cut between David Strettle and Ernst Joubert and then wrestled his way through Alex Goode's tackle to score Harlequins' second try.
Farrell and Evans each missed a shot at goal before the England fly-half brought Saracens back to within two points with his fourth penalty.
Harlequins were forced to make a change at the interval with fly-half Rory Clegg replacing Evans. The newcomer managed one penalty from three attempts.
Then Care struck. Brown made the half break and offloaded to Tom Guest, who charged into the 22, drew Alex Goode and sent the exiled England scrum-half over for the try.
Saracens then laid siege on the Harlequins line, forcing the Premiership leaders into lung-bursting defence for almost all of the final 20 minutes.
Goode's elusive break launched Saracens into the Quins half and Jackson Wray took the ball on to build the pressure but the final pass just escaped Strettle down the left.
Saracens secured the lineout and drove for the line, building the pressure on Harlequins until Marler was penalised and sent to the sin-bin.
Lowe was Harlequins' defensive hero, making those two try-saving tackles to keep Saracens out.
The first was on Tagicakibau, when he combined with Williams to drive the Saracens wing into touch after Strettle and Hodgson had combined in midfield.
Still Saracens pounded away and still Harlequins resisted, with Lowe tackling Wyles into touch after Farrell and Strettle had created the overlap.
Harlequins were reduced to 13 men when Care was sent to the sin-bin for running a cynical off-side line and finally Saracens managed to breach the defence.
Saracens opted for the scrum and replacement Richard Wigglesworth stole over the line to tee up a grandstand finish.
Marler returned and was almost immediately replaced in the sin-bin by Easter, who was penalised for pulling a lineout down, but Harlequins survived to claim a significant victory.
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